242 lines
6.2 KiB
OCaml
242 lines
6.2 KiB
OCaml
open Qptypes;;
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open Qputils;;
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open Sexplib.Std;;
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module Nuclei_by_hand : sig
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type t =
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{ nucl_num : Nucl_number.t ;
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nucl_label : Element.t array;
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nucl_charge : Charge.t array;
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nucl_coord : Point3d.t array;
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} [@@deriving sexp]
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;;
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val read : unit -> t option
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val write : t -> unit
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val to_string : t -> string
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val to_atom_list : t -> Atom.t list
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val to_rst : t -> Rst_string.t
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val of_rst : Rst_string.t -> t option
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end = struct
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type t =
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{ nucl_num : Nucl_number.t ;
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nucl_label : Element.t array;
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nucl_charge : Charge.t array;
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nucl_coord : Point3d.t array;
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} [@@deriving sexp]
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;;
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let get_default = Qpackage.get_ezfio_default "nuclei";;
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let read_nucl_num () =
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let nmax = Nucl_number.get_max () in
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Nucl_number.of_int ~max:nmax nmax
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;;
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let write_nucl_num n =
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Nucl_number.to_int n
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|> Ezfio.set_nuclei_nucl_num
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;;
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let read_nucl_label () =
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Ezfio.get_nuclei_nucl_label ()
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|> Ezfio.flattened_ezfio
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|> Array.map Element.of_string
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;;
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let write_nucl_label ~nucl_num labels =
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let nucl_num =
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Nucl_number.to_int nucl_num
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in
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let labels =
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Array.to_list labels
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|> list_map Element.to_string
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in
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Ezfio.ezfio_array_of_list ~rank:1
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~dim:[| nucl_num |] ~data:labels
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|> Ezfio.set_nuclei_nucl_label
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;;
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let read_nucl_charge () =
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Ezfio.get_nuclei_nucl_charge ()
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|> Ezfio.flattened_ezfio
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|> Array.map Charge.of_float
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;;
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let write_nucl_charge ~nucl_num charges =
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let nucl_num =
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Nucl_number.to_int nucl_num
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in
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let charges =
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Array.to_list charges
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|> list_map Charge.to_float
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in
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Ezfio.ezfio_array_of_list ~rank:1
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~dim:[| nucl_num |] ~data:charges
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|> Ezfio.set_nuclei_nucl_charge
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;;
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let read_nucl_coord () =
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let nucl_num = Nucl_number.to_int (read_nucl_num ()) in
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let raw_data =
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Ezfio.get_nuclei_nucl_coord()
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|> Ezfio.flattened_ezfio
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in
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let zero = Point3d.of_string ~units:Units.Bohr "0. 0. 0." in
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let result = Array.make nucl_num zero in
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for i=0 to (nucl_num-1)
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do
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result.(i) <- Point3d.({ x=raw_data.(i);
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y=raw_data.(nucl_num+i);
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z=raw_data.(2*nucl_num+i); });
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done;
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result
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;;
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let write_nucl_coord ~nucl_num coord =
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let nucl_num =
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Nucl_number.to_int nucl_num
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in
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let coord = Array.to_list coord in
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let coord =
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(list_map (fun x-> x.Point3d.x) coord) @
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(list_map (fun x-> x.Point3d.y) coord) @
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(list_map (fun x-> x.Point3d.z) coord)
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in
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Ezfio.ezfio_array_of_list ~rank:2
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~dim:[| nucl_num ; 3 |] ~data:coord
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|> Ezfio.set_nuclei_nucl_coord
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;;
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let read () =
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if (Ezfio.has_nuclei_nucl_num ()) then
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Some
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{ nucl_num = read_nucl_num ();
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nucl_label = read_nucl_label () ;
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nucl_charge = read_nucl_charge ();
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nucl_coord = read_nucl_coord ();
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}
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else
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None
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;;
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let write { nucl_num ;
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nucl_label ;
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nucl_charge ;
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nucl_coord ;
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} =
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write_nucl_num nucl_num ;
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write_nucl_label ~nucl_num:nucl_num nucl_label;
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write_nucl_charge ~nucl_num:nucl_num nucl_charge;
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write_nucl_coord ~nucl_num:nucl_num nucl_coord;
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;;
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let to_atom_list b =
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let rec loop accu (coord, charge, label) = function
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| -1 -> accu
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| i ->
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let atom =
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{ Atom.element = label.(i) ;
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Atom.charge = charge.(i) ;
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Atom.coord = coord.(i) ;
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}
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in
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loop (atom::accu) (coord, charge, label) (i-1)
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in
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loop [] (b.nucl_coord, b.nucl_charge, b.nucl_label)
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( (Nucl_number.to_int b.nucl_num) - 1)
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;;
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let to_string b =
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Printf.sprintf "
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nucl_num = %s
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nucl_label = %s
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nucl_charge = %s
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nucl_coord = %s
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"
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(Nucl_number.to_string b.nucl_num)
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(b.nucl_label |> Array.to_list |> list_map
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(Element.to_string) |> String.concat ", " )
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(b.nucl_charge |> Array.to_list |> list_map
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(Charge.to_string) |> String.concat ", " )
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(b.nucl_coord |> Array.to_list |> list_map
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(Point3d.to_string ~units:Units.Bohr) |> String.concat "\n" )
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;;
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let to_rst b =
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let nucl_num = Nucl_number.to_int b.nucl_num in
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let text =
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( Printf.sprintf " %d\n "
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nucl_num
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) :: (
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List.init nucl_num (fun i->
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Printf.sprintf " %-3s %3d %s"
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(b.nucl_label.(i) |> Element.to_string)
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(b.nucl_charge.(i) |> Charge.to_int )
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(b.nucl_coord.(i) |> Point3d.to_string ~units:Units.Angstrom) )
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) |> String.concat "\n"
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in
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Printf.sprintf "
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Nuclear coordinates in xyz format (Angstroms) ::
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%s
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" text
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|> Rst_string.of_string
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;;
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let of_rst s =
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let l = Rst_string.to_string s
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|> String_ext.split ~on:'\n'
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in
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(* Find lines containing the xyz data *)
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let rec extract_begin = function
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| [] -> raise Not_found
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| line::tail ->
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let line = String.trim line in
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if (String.length line > 3) &&
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(String.sub line ((String.length line)-2) 2 = "::") then
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tail
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else
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extract_begin tail
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in
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(* Create a list of Atom.t *)
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let nmax = Nucl_number.get_max () in
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let atom_list =
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match (extract_begin l) with
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| _ :: nucl_num :: title :: lines ->
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begin
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let nucl_num = nucl_num
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|> String.trim
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|> int_of_string
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|> Nucl_number.of_int ~max:nmax
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and lines = Array.of_list lines
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in
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List.init (Nucl_number.to_int nucl_num) (fun i ->
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Atom.of_string ~units:Units.Angstrom lines.(i))
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end
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| _ -> failwith "Error in xyz format"
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in
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(* Create the Nuclei.t data structure *)
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let result =
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{ nucl_num = List.length atom_list
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|> Nucl_number.of_int ~max:nmax;
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nucl_label = list_map (fun x ->
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x.Atom.element) atom_list |> Array.of_list ;
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nucl_charge = list_map (fun x ->
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x.Atom.charge ) atom_list |> Array.of_list ;
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nucl_coord = list_map (fun x ->
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x.Atom.coord ) atom_list |> Array.of_list ;
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}
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in Some result
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;;
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end
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